Can you say cliffhanger? (It's not that hard to pronounce. Even the kid with bees in his mouth could say it.) At the end of this installment, Golan the wight is killed when Jacob gets up the courage to shoot the man in the neck. Whoa. Golan throws the cage containing Miss Peregrine and her mentor, Miss Avocet, into the ocean, but Emma and Jacob are able to recover Miss Peregrine, who somehow gets out of the cage, but a German U-Boat takes the other cage away.
The bad guys are kidnapping ymbrynes as part of a vaguely defined effort to achieve eternal life, and the peculiar children of Miss Peregrine's home (for peculiar children) decide they have to stop them. They really don't have a choice because Miss Peregrine is stuck in bird form (of a peregrine, of course), which causes their time loop to fail and the titular home for peculiar children to be wiped out by a bomb.
Boom. What an ending. The good thing is that you can find out what happens after the smoke clears by grabbing the second book, Hollow City, which was published in 2014.